In the development of a drug, the binding between a protein as one of the macromolecular compounds constituting a living body and a drug candidate agent, is evaluated. That is, a drug having a low affinity with respect to a protein is not appropriate as a drug candidate agent, and such drugs having a low affinity are excluded from the drug candidate agent. Moreover, as an evaluation method for the abovementioned affinity, X-ray structural analysis or a classical molecular dynamics method is generally used.
For example, in a prior art document below, there is disclosed study results of the binding mechanism between adenylate cyclase (type II) as a protein and forskolin as a drug candidate agent, as a case of affinity analysis using the classical molecular dynamics method. In this prior art document, by calculating each internal energy (potential energy+kinetic energy) of analytical models (systems) where various drug candidate agents such as forskolin are placed at the centre of the active site of adenylate cyclase using the classical molecular dynamics method, those having a relatively small internal energy (that is, those that stabilize the system energetically) are extracted as drug candidate agents having excellent affinity with respect to adenylate cyclase. At the same time, the document examines the binding site of forskolin, which is extracted as such and which is one of the drug candidate agents, with respect to adenylate cyclase.
[Non Patent Document 1]    Takeshi Onda et al., J. Bio. Chem., 276 (2001) 47785-47793